Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold82
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2626005
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.31
Warning! 196346 characters in sequence are not A, C, G, or T
File 17 of 17
Found at i:2480329 original size:23 final size:23
Alignment explanation
Indices: 2480303--2480454 Score: 67
Period size: 22 Copynumber: 6.7 Consensus size: 23
2480293 TAAGACATTA
*
2480303 ATAAGTATTTATATATATAAATT
1 ATAAATATTTATATATATAAATT
2480326 ATAAATATTT-TATA-AT--A-T
1 ATAAATATTTATATATATAAATT
*
2480344 ATAATATATGTTATGTATTATAAAATGT
1 ATAA-ATAT-TTATATA-TAT-AAAT-T
2480372 ATATAATATTTA-ATATAT-AATT
1 ATA-AATATTTATATATATAAATT
* * *
2480394 ATTACAT-TATTATTTTTA-AATATT
1 A-TAAATAT-TTATATATATAA-ATT
* *
2480418 TTAAATA-TTATATAT-TAAATA
1 ATAAATATTTATATATATAAATT
2480439 ATTAAATATTT-TATAT
1 A-TAAATATTTATATAT
2480455 TTATCATTCA
Statistics
Matches: 97, Mismatches: 12, Indels: 41
0.65 0.08 0.27
Matches are distributed among these distances:
18 5 0.05
19 5 0.05
20 2 0.02
21 8 0.08
22 30 0.31
23 26 0.27
24 3 0.03
25 3 0.03
26 3 0.03
27 3 0.03
28 8 0.08
29 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.51
Consensus pattern (23 bp):
ATAAATATTTATATATATAAATT
Found at i:2481273 original size:38 final size:38
Alignment explanation
Indices: 2481229--2481331 Score: 99
Period size: 40 Copynumber: 2.7 Consensus size: 38
2481219 GATTTGATTA
2481229 AATTTAAATTATTATTTAATTAATAAA-AAATTTATTTT
1 AATTTAAATTATTATTTAATTAATAAATAAATTT-TTTT
**
2481267 AATTTAAATTAATTATAAAAATATAA-AAATAAATTTTTTT
1 AATTTAAATT-ATTAT-TTAAT-TAATAAATAAATTTTTTT
*
2481307 AATTTTAATGT-TT-TTTAA-TAATAAA
1 AATTTAAAT-TATTATTTAATTAATAAA
2481332 GCAAAATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
35 3 0.06
36 3 0.06
37 2 0.04
38 11 0.20
39 7 0.13
40 18 0.33
41 10 0.19
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.50
Consensus pattern (38 bp):
AATTTAAATTATTATTTAATTAATAAATAAATTTTTTT
Found at i:2481661 original size:12 final size:12
Alignment explanation
Indices: 2481644--2481671 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2481634 CTCTTTGAGA
2481644 TTTTTTTTTAAT
1 TTTTTTTTTAAT
2481656 TTTTTTTTTAAT
1 TTTTTTTTTAAT
2481668 TTTT
1 TTTT
2481672 GGTGCTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTTTAAT
Found at i:2481921 original size:19 final size:18
Alignment explanation
Indices: 2481890--2481925 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2481880 CATGTTAATT
2481890 TATCTATTAATATATTTA
1 TATCTATTAATATATTTA
*
2481908 TATCATATTTATATATTT
1 TATC-TATTAATATATTT
2481926 TTATATGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (18 bp):
TATCTATTAATATATTTA
Found at i:2482057 original size:25 final size:26
Alignment explanation
Indices: 2482015--2482067 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
2482005 TCTATACATA
*
2482015 TAATTTTTTATATTATA-TTATATTT
1 TAATTTTTTATATAATATTTATATTT
2482040 TAATTATTTT-TATAATATTTATATTT
1 TAATT-TTTTATATAATATTTATATTT
2482066 TA
1 TA
2482068 TAATTATATC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (26 bp):
TAATTTTTTATATAATATTTATATTT
Found at i:2482068 original size:16 final size:16
Alignment explanation
Indices: 2481972--2482071 Score: 54
Period size: 16 Copynumber: 6.6 Consensus size: 16
2481962 TTTTATAATT
*
2481972 TTTTATAA-ATTAATA
1 TTTTATAATATTTATA
* * *
2481987 ATTTATAATATATAAA
1 TTTTATAATATTTATA
* *
2482003 TTTCTATACATA-TAATT
1 TTT-TATA-ATATTTATA
*
2482020 TTTTATATTATATTATA
1 TTTTATAATAT-TTATA
2482037 -TTT-T-A-A-TTAT-
1 TTTTATAATATTTATA
2482047 TTTTATAATATTTATA
1 TTTTATAATATTTATA
2482063 TTTTATAAT
1 TTTTATAAT
2482072 TATATCATAT
Statistics
Matches: 61, Mismatches: 13, Indels: 21
0.64 0.14 0.22
Matches are distributed among these distances:
11 7 0.11
12 1 0.02
13 2 0.03
14 1 0.02
15 14 0.23
16 22 0.36
17 11 0.18
18 3 0.05
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTATAATATTTATA
Found at i:2483286 original size:24 final size:25
Alignment explanation
Indices: 2483273--2483318 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
2483263 TATTTTTTAT
2483273 AATTTAATTTAATTAATTATTTAAA
1 AATTTAATTTAATTAATTATTTAAA
*
2483298 AATTTAA-TTAA-CAATTATTTA
1 AATTTAATTTAATTAATTATTTA
2483319 GTTCAATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 4 0.20
25 7 0.35
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
AATTTAATTTAATTAATTATTTAAA
Found at i:2486257 original size:24 final size:25
Alignment explanation
Indices: 2486221--2486267 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
2486211 AATTAAAAAA
*
2486221 TAATAAAATATATTTAA-ATATAAT
1 TAATAAAACATATTTAATATATAAT
*
2486245 TAATATAACATATTTAATATATA
1 TAATAAAACATATTTAATATATA
2486268 TTATATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
TAATAAAACATATTTAATATATAAT
Found at i:2487008 original size:14 final size:14
Alignment explanation
Indices: 2486989--2487047 Score: 54
Period size: 14 Copynumber: 4.5 Consensus size: 14
2486979 ATATAATGAA
2486989 TATATTAAATATAT
1 TATATTAAATATAT
*
2487003 TATATT-AAT-CA-
1 TATATTAAATATAT
*
2487014 TAT-TTAAATATTT
1 TATATTAAATATAT
* *
2487027 TATATTATATTTAT
1 TATATTAAATATAT
2487041 TATATTA
1 TATATTA
2487048 TTTTTATATT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
10 2 0.06
11 6 0.17
12 1 0.03
13 6 0.17
14 20 0.57
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (14 bp):
TATATTAAATATAT
Found at i:2487030 original size:29 final size:25
Alignment explanation
Indices: 2486998--2487064 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 25
2486988 ATATATTAAA
2486998 TATATTATATTAATCATATTTAAATATTT
1 TATATTATATTAATCATA-TT--AT-TTT
* *
2487027 TATATTATATTTATTATATTATTTT
1 TATATTATATTAATCATATTATTTT
2487052 TATATT-TATTAAT
1 TATATTATATTAAT
2487065 ACTTATATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 6 0.17
25 9 0.26
26 2 0.06
28 2 0.06
29 16 0.46
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (25 bp):
TATATTATATTAATCATATTATTTT
Found at i:2487038 original size:12 final size:12
Alignment explanation
Indices: 2487021--2487091 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 12
2487011 TCATATTTAA
2487021 ATATTTTATATT
1 ATATTTTATATT
2487033 ATATTTATTATATT
1 ATA-TT-TTATATT
2487047 AT-TTTTATATT
1 ATATTTTATATT
*
2487058 -TA-TTAATACTT
1 ATATTTTATA-TT
*
2487069 ATA-TTTATGTT
1 ATATTTTATATT
2487080 ATATTTTCATAT
1 ATATTTT-ATAT
2487092 GATACCAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
10 6 0.12
11 14 0.29
12 14 0.29
13 5 0.10
14 9 0.19
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (12 bp):
ATATTTTATATT
Found at i:2487048 original size:14 final size:14
Alignment explanation
Indices: 2486998--2487054 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
2486988 ATATATTAAA
*
2486998 TATATTATATTAAT
1 TATATTATATTTAT
* *
2487012 CATATTTAAATATT-T
1 TATA-TTATAT-TTAT
2487027 TATATTATATTTAT
1 TATATTATATTTAT
*
2487041 TATATTATTTTTAT
1 TATATTATATTTAT
2487055 ATTTATTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
13 2 0.06
14 22 0.65
15 9 0.26
16 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (14 bp):
TATATTATATTTAT
Found at i:2487054 original size:20 final size:22
Alignment explanation
Indices: 2487031--2487076 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
2487021 ATATTTTATA
*
2487031 TTATATTTATT-ATA-TTATTT
1 TTATATTTATTAATACTTATAT
2487051 TTATATTTATTAATACTTATAT
1 TTATATTTATTAATACTTATAT
2487073 TTAT
1 TTAT
2487077 GTTATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.48
21 3 0.13
22 9 0.39
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATATTTATTAATACTTATAT
Found at i:2487893 original size:41 final size:41
Alignment explanation
Indices: 2487815--2487893 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
2487805 TAAAAAATAT
* ** *
2487815 AATATAAATAAATTTAAATAAATTTTGATTATCTATTTACA
1 AATATAAAAAAATTTAAATAAATTTAAATTATATATTTACA
*
2487856 AATATAAAAAAATTTAGATAAAATTTAAATT-TATATTT
1 AATATAAAAAAATTTAAAT-AAATTTAAATTATATATTT
2487894 CAAGTCAGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 23 0.72
42 9 0.28
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.43
Consensus pattern (41 bp):
AATATAAAAAAATTTAAATAAATTTAAATTATATATTTACA
Found at i:2488326 original size:29 final size:29
Alignment explanation
Indices: 2488273--2488349 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
2488263 AATTTTGAAT
*
2488273 ATGAAATAAAT-TATAATATAATATAAAAA
1 ATGATATAAATATATAATATAATAT-AAAA
*
2488302 ATGATATAAATATATAA-ATATTATAAAA
1 ATGATATAAATATATAATATAATATAAAA
* *
2488330 TTTATATAAAATATATAATA
1 ATGATAT-AAATATATAATA
2488350 ATTTAAATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 9 0.22
29 26 0.63
30 6 0.15
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (29 bp):
ATGATATAAATATATAATATAATATAAAA
Found at i:2488330 original size:18 final size:18
Alignment explanation
Indices: 2488278--2488362 Score: 52
Period size: 18 Copynumber: 4.6 Consensus size: 18
2488268 TGAATATGAA
*
2488278 ATAAATTATAATATAATAT
1 ATAAA-TATAATAAAATAT
* *
2488297 A-AAAAATGATATAAATAT
1 ATAAATATAATA-AAATAT
*
2488315 ATAAATATTATAAAATTTAT
1 ATAAATATAATAAAA--TAT
2488335 ATAAA-ATATATAATAAT-T
1 ATAAATATA-ATAA-AATAT
2488353 -TAAATATAAT
1 ATAAATATAAT
2488363 TATATTATAA
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
17 11 0.21
18 16 0.30
19 12 0.23
20 12 0.23
21 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (18 bp):
ATAAATATAATAAAATAT
Found at i:2491686 original size:24 final size:22
Alignment explanation
Indices: 2491630--2491678 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
2491620 TGGACATGTT
2491630 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
2491652 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
2491674 AAAAA
1 AAAAA
2491679 AATGCATGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.67, C:0.08, G:0.08, T:0.16
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:2492643 original size:20 final size:20
Alignment explanation
Indices: 2492596--2492670 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
2492586 AAAAAGACAT
*
2492596 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
2492615 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
2492636 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
2492656 AATGTATCGATACAT
1 AATGTATCGATACAT
2492671 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:2492664 original size:40 final size:39
Alignment explanation
Indices: 2492593--2492670 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
2492583 GGTAAAAAGA
* *
2492593 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
2492632 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
2492671 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:2493018 original size:20 final size:20
Alignment explanation
Indices: 2492973--2493026 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
2492963 CAAGGAAATG
*
2492973 TATCGATACATACTTATAATTG
1 TATCGATACAT--TTATAATTA
*
2492995 TATCGATACATTTATCATTA
1 TATCGATACATTTATAATTA
*
2493015 TATCAATACATT
1 TATCGATACATT
2493027 CTGGGTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 18 0.62
22 11 0.38
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.43
Consensus pattern (20 bp):
TATCGATACATTTATAATTA
Found at i:2494162 original size:61 final size:61
Alignment explanation
Indices: 2494067--2494541 Score: 506
Period size: 61 Copynumber: 7.6 Consensus size: 61
2494057 AATCTTTTAT
* * * * *
2494067 CCTTTTAGTCCTCAAAGAGAATGACGCCTTCTCTTTTTAAAGCCCACATAAGTTGGTGACA
1 CCTTTTAGTCCTCAAAGAGTAGGACGCTTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCA
* *
2494128 CCTTTCAGTCCTCAAAGAGTAGGACGCTTTCTCTTTTTAAAGCCCACACAAGTTAGTGGCA
1 CCTTTTAGTCCTCAAAGAGTAGGACGCTTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
2494189 CCTTTTAGTCCTCAAAGAGCATGACACTTTTCTTTTTTCTTTTAAAGCCCACACAAGTTGGTGGC
1 CCTTTTAGTCCTCAAAGAGTAGGACGC-TTTC---TCT-TTTTAAAGCCCACACAAGTTGGTGGC
2494254 A
61 A
* * * * * *
2494255 CCTTTTAGTCCTTAAAGA-TCATGATGCCTTT-TCTATTTAAAGCCCACACAAGTTAGTGGCG
1 CCTTTTAGTCCTCAAAGAGT-AGGACG-CTTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
2494316 CCTTTTACTCCTTAAAGAGTAGGACACCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGTAGGACGCTTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
2494377 CCTTTTAGTCCTCAAAGAGCATGATGCCTTT-TCTTTTCAAAGCCCACATAAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGTAGGACG-CTTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
2494438 CCTTTTAGTCCTCAAAGAGTGGGACATTTCTTTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGTAGGAC---GCTTTCTCT-TTTTAAAGCCCACACAAGTTGGTGGCA
* * *
2494503 CCTTTTAGTTCTCAAAGAGTAGGATGCCTCTCTCTTTTT
1 CCTTTTAGTCCTCAAAGAGTAGGACG-CTTTCTCTTTTT
2494542 TTATCTTAAA
Statistics
Matches: 344, Mismatches: 54, Indels: 31
0.80 0.13 0.07
Matches are distributed among these distances:
60 3 0.01
61 217 0.63
62 14 0.04
63 9 0.03
64 2 0.01
65 48 0.14
66 50 0.15
67 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (61 bp):
CCTTTTAGTCCTCAAAGAGTAGGACGCTTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:2494438 original size:249 final size:248
Alignment explanation
Indices: 2494067--2494520 Score: 687
Period size: 249 Copynumber: 1.8 Consensus size: 248
2494057 AATCTTTTAT
* * * *
2494067 CCTTTTAGTCCTCAAAGAGAATGACGCCTTCTCTTTTTAAAGCCCACATAAGTTGGTGACACCTT
1 CCTTTTACTCCTCAAAGAGAAGGACACCTTCTCTTTTTAAAGCCCACACAAGTTGGTGACACCTT
* *
2494132 TCAGTCCTCAAAGAGTAGGACGCTTTCTCTTTTTAAAGCCCACACAAGTTAGTGGCACCTTTTAG
66 TCAGTCCTCAAAGAGCAGGACGCTTTCTCTTTTCAAAGCCCACACAAGTTAGTGGCACCTTTTAG
* *
2494197 TCCTCAAAGAGCATGACACTTTTC-TTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
131 TCCTCAAAGAG--TGACACATTTCTTTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTT
*
2494261 AGTCCTTAAAGATCATGATGCCTTTTCTATTTAAAGCCCACACAAGTTAGTGGCG
194 AGTCCTCAAAGATCATGATGCCTTTTCTATTTAAAGCCCACACAAGTTAGTGGCG
* * *
2494316 CCTTTTACTCCTTAAAGAGTAGGACACCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTT
1 CCTTTTACTCCTCAAAGAGAAGGACACCTTCTCTTTTTAAAGCCCACACAAGTTGGTGACACCTT
* * * * *
2494381 TTAGTCCTCAAAGAGCATGATGCCTTT-TCTTTTCAAAGCCCACATAAGTTGGTGGCACCTTTTA
66 TCAGTCCTCAAAGAGCAGGACG-CTTTCTCTTTTCAAAGCCCACACAAGTTAGTGGCACCTTTTA
**
2494445 GTCCTCAAAGAGTGGGACATTTCTTTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTTA
130 GTCCTCAAAGAGTGACACATTTCTTTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTTA
*
2494510 GTTCTCAAAGA
195 GTCCTCAAAGA
2494521 GTAGGATGCC
Statistics
Matches: 183, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
247 8 0.04
248 49 0.27
249 122 0.67
250 4 0.02
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (248 bp):
CCTTTTACTCCTCAAAGAGAAGGACACCTTCTCTTTTTAAAGCCCACACAAGTTGGTGACACCTT
TCAGTCCTCAAAGAGCAGGACGCTTTCTCTTTTCAAAGCCCACACAAGTTAGTGGCACCTTTTAG
TCCTCAAAGAGTGACACATTTCTTTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTTAG
TCCTCAAAGATCATGATGCCTTTTCTATTTAAAGCCCACACAAGTTAGTGGCG
Found at i:2494539 original size:188 final size:182
Alignment explanation
Indices: 2494067--2494541 Score: 571
Period size: 188 Copynumber: 2.5 Consensus size: 182
2494057 AATCTTTTAT
** * * * *
2494067 CCTTTTAGTCCTCAAAGAGAATGACGCCTTCTCTTTTTAAAGCCCACATAAGTTGGTGACACCTT
1 CCTTTTAGTCCTCAAAGATCAT-ATGCCTTTTC-TTTTAAAGCCCACACAAGTTGGTGGCACCTT
* *
2494132 TCAGTCCTCAAAGAGTAGGACGCTTTCTCTTTTTAAAGCCCACACAAGTTAGTGGCACCTTTTAG
64 TTAGTCCTCAAAGAGTAGGACGCCTTCTCTTTTTAAAGCCCACACAAGTTAGTGGCACCTTTTAG
2494197 TCCTCAAAGAGCATGACACTTTTCTTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
129 TCCTCAAAGAGCATGACACTTTTC-TTTTTC---TAAAGCCCACACAAGTTGGTGGCA
* * *
2494255 CCTTTTAGTCCTTAAAGATCATGATGCCTTTTCTATTTAAAGCCCACACAAGTTAGTGGCGCCTT
1 CCTTTTAGTCCTCAAAGATCAT-ATGCCTTTTCT-TTTAAAGCCCACACAAGTTGGTGGCACCTT
* * * *
2494320 TTACTCCTTAAAGAGTAGGACACCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAG
64 TTAGTCCTCAAAGAGTAGGACGCCTTCTCTTTTTAAAGCCCACACAAGTTAGTGGCACCTTTTAG
*
2494385 TCCTCAAAGAGCATGATGC-CTTTTC-TTTTC-AAAGCCCACATAAGTTGGTGGCA
129 TCCTCAAAGAGCATGA--CACTTTTCTTTTTCTAAAGCCCACACAAGTTGGTGGCA
* * *
2494438 CCTTTTAGTCCTCAAAGAGTGGGACAT-TTCTTTTTTTCTTTTAAAGCCCACACAAGCTGGTGGC
1 CCTTTTAGTCCTCAAAGA-T----CATATGC--CTTTTCTTTTAAAGCCCACACAAGTTGGTGGC
* *
2494502 ACCTTTTAGTTCTCAAAGAGTAGGATGCCTCTCTCTTTTT
59 ACCTTTTAGTCCTCAAAGAGTAGGACGCCT-TCTCTTTTT
2494542 TTATCTTAAA
Statistics
Matches: 249, Mismatches: 27, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
183 39 0.16
184 1 0.00
186 2 0.01
187 53 0.21
188 147 0.59
189 6 0.02
190 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (182 bp):
CCTTTTAGTCCTCAAAGATCATATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
AGTCCTCAAAGAGTAGGACGCCTTCTCTTTTTAAAGCCCACACAAGTTAGTGGCACCTTTTAGTC
CTCAAAGAGCATGACACTTTTCTTTTTCTAAAGCCCACACAAGTTGGTGGCA
Found at i:2495166 original size:22 final size:20
Alignment explanation
Indices: 2495138--2495193 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
2495128 GCCAAGGAAA
2495138 TGTATCGATACATACTTATAAT
1 TGTATCGATACAT--TTATAAT
*
2495160 TGTATCGATACATTTATCAT
1 TGTATCGATACATTTATAAT
*
2495180 AGTATCGATACATT
1 TGTATCGATACATT
2495194 CTGGTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 19 0.59
22 13 0.41
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTTATAAT
Found at i:2496282 original size:10 final size:9
Alignment explanation
Indices: 2496237--2496284 Score: 51
Period size: 10 Copynumber: 5.0 Consensus size: 9
2496227 ATAAAATACA
*
2496237 AAAAAAAAG
1 AAAAAAAAT
2496246 ACAAAAAAAT
1 A-AAAAAAAT
2496256 ATAAAAAAAT
1 A-AAAAAAAT
*
2496266 AATAAAAAGT
1 AA-AAAAAAT
2496276 AAAAAAAAT
1 AAAAAAAAT
2496285 GATGAGTGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 8 0.24
10 25 0.76
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.12
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:2506458 original size:48 final size:48
Alignment explanation
Indices: 2506396--2506527 Score: 192
Period size: 48 Copynumber: 2.8 Consensus size: 48
2506386 CGAGGAGTGC
** * * * *
2506396 CAATGTGCCAATTCAAGTCCAACAACATTGAGCTAAGGGAAAAGTGGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGAAAAAGTGGA
* *
2506444 CAATGTGCTGATTCAAGGCTAGCGACATTAAGCTAAGGAAAAAGTGGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGAAAAAGTGGA
2506492 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAA
2506528 TAAAGGTGCC
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 74 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.20
Consensus pattern (48 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGAAAAAGTGGA
Found at i:2506965 original size:32 final size:32
Alignment explanation
Indices: 2506752--2508441 Score: 1424
Period size: 32 Copynumber: 55.5 Consensus size: 32
2506742 CTTTGAAAAT
*
2506752 TTGCCACTGAC-T-TGTGGGCTTTGAAA--AG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* *
2506780 TTGCCACTGAC-T-TGTGGGCTTGGAAA--AG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* ** *
2506808 ATGCCATTGACTTG-G-GGGTTTTGAAA--AG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* * * *
2506836 ATGCCACCGACTTAT-T-GACATTGAAA-G-G
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* *
2506864 ATGCCACTGAC-T-TGTGGGCTTTGAAA-G-G
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* **
2506892 GTGCCATTGAC-T-TGTGGGCTTTGAAA--AG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* * *
2506920 ATGCCATCAACTTGTGTGGGCTTTGAAATGAG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* * *
2506952 TTGCCACCGACTTGTGTAGGCTTTCAAATGGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* *
2506984 TTGCCACCAACTTGTATGGGCTTTGAAAT-AGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGA-G
*
2507016 TTGCCACCAACTTGTGTGGGCTTTGAAATGAG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* *
2507048 TTACCACCGACTTGTGTGGGCTTTGGAATGA-
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
**
2507079 -TGCCACAAAC-T-TGTGGGCTTTGAAATTG-G
1 TTGCCACCGACTTGTGTGGGCTTTGAAA-TGAG
*
2507108 TTGCCACAGACTTGTGTGGGCTTTGAAAT-AGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGA-G
* *
2507140 TTGCCACCAACTTGTGTGGACTTTGAAATG-G
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* * *
2507171 CTTGCCACCAACTTGTGTGTGCTTTCAAATGAG
1 -TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* **
2507204 TTGCCACCGACTTATGTGGGCTTTGGGATGA-
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* * *
2507235 -T-CCACTGAC-T-TGTGGGCTTTGGAATGGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* *
2507263 TTGCCACCAACTTGTGTGGGCTTTGAAATGGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* * *
2507295 TTGCCACCAACTTGTGTGGACTTTGAAATGGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* * *
2507327 TTGCCACCAACTTGTATGGGCTTTCAAATGAG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* * *
2507359 TTGCCACTGA-TATATGTGGGCTTTGGAATGA-
1 TTGCCACCGACT-TGTGTGGGCTTTGAAATGAG
* *
2507390 -T-CCACTGAC-T-TGTGGGCTTTGAAATGGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* *
2507418 TTGCCACAGACTTGTGTGGGCTTTGAAATGGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* * *
2507450 TTGCCATCAACTTGTGTGGGCTTTGAAATGGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* *
2507482 TTGCCACCAACTTGTGTGGGCTTTCAAATGAG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
*
2507514 TTGCCACCGACTTATGTGGGCTTTGAAA--AG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* * ** *
2507544 ATGCCACTGAC-T-TGTGAACATTGAAA-G-G
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* *
2507572 ATGCCACTGAC-T-TGTGGGCTTTGAAA-GAG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* * *
2507601 -TGTCACTGAC-T-TGTGGGCTTGGAAA--AG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* *
2507628 GTGCCACTGAC-T-TGTGGGCTTTGAAA-G-G
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* * * *
2507656 GTGCCACTGAC-T-TATGGGCTTTGAAATGGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* *
2507686 TTG-CACCAACTTGTGTGGGCTTTGAAATGGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* ** * *
2507717 TTACCACTAATTTGTGTGGTCTTTGAAATGAG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* * *
2507749 TTGCCACCAACTTGTGTGGGCTTTCAAATGGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
*
2507781 TTGCCACCAACTTGTGTGGGCTTTGAAAT-AGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGA-G
* * *
2507813 TTGCCACCAATTTGTGTGGGCTTTGAAATGGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
*
2507845 TTGCCACCGACTTGTGTGGGCTTTCAAATGAG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
*
2507877 TTGCCCCCGACTTGTGTGGGCTTTGAAA--AG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* * *
2507907 ATGCCACCGAC-T-TGTGGACATTGAAA-G-G
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* **
2507935 ATGCCAGTGAC-T-TGTGGGCTTTGAAA--AG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* * * *
2507963 ATGCCCCCGACTTGTGTAGGCTTTGAAATGGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
*
2507995 TTGCCACCAACTTGTGTGGGCTTTGAAATGAG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* * * * *
2508027 TTTCCACCAAC-T-TGTGGACATT-AAA-AAG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* * *
2508055 ATGCCACTGAC-T-TGTGGGCTTTGAAATGGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* *
2508085 TTGCCACCAACTTGTGTGGGCTTTGAAATGGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
*
2508117 TTGCCACCAACTTGTGTGGGCTTTGAAATGAG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* * * *
2508149 TTGCCACTGACTTGTGTGGACTTTCAAATGGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* *
2508181 TTGCCACCAACTTATGTGGGCTTTGAAAT-AGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGA-G
* *
2508213 TTGCCACCAACTTGTGTGGGCTTTGAAATGGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* * *
2508245 TTGCCATCAACTTGTGTGGGCTTTGAAATGGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
*
2508277 TTGCCACCGACTTGTGTGAGCTTTGAAA--AG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* * *
2508307 ATGCCACTGAC-T-TGTGGGCTTTGAAATGGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* *
2508337 TTGCCACCGACTTATGTGAGCTTTGAAA--AG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* *
2508367 ATGCCACCGAC-T-TGTGGGCTTTGAAATGGG
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
*
2508397 TTGCCACAGACTTGTGTGGG-TTTGAAAT-A-
1 TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* *
2508426 ATGCCACTGACTTGTG
1 TTGCCACCGACTTGTG
2508442 GATTTGACAT
Statistics
Matches: 1409, Mismatches: 186, Indels: 133
0.82 0.11 0.08
Matches are distributed among these distances:
26 1 0.00
27 34 0.02
28 330 0.23
29 54 0.04
30 142 0.10
31 37 0.03
32 809 0.57
33 2 0.00
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (32 bp):
TTGCCACCGACTTGTGTGGGCTTTGAAATGAG
Found at i:2518404 original size:15 final size:15
Alignment explanation
Indices: 2518384--2518412 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2518374 CTAGAGTTAG
2518384 GAGTTGCAGTTGTTT
1 GAGTTGCAGTTGTTT
2518399 GAGTTGCAGTTGTT
1 GAGTTGCAGTTGTT
2518413 CGAATTCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.34, T:0.45
Consensus pattern (15 bp):
GAGTTGCAGTTGTTT
Found at i:2518965 original size:27 final size:27
Alignment explanation
Indices: 2518836--2519440 Score: 739
Period size: 27 Copynumber: 22.2 Consensus size: 27
2518826 TTTCTTTTCA
2518836 AAGTCCACAACTCCGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
2518863 AAAGTTCACAACTCCGTGGCATCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
*
2518891 AAAGTTCACAACTCCGTGGCATCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
* *
2518919 AAAATCTACAACTCCGTGGCATCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
* *
2518947 AAGTCCACAACTTCATGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* * *
2518974 AAGTCCACAACTTCGTGCCATCATTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
** * *
2519001 AAAGTCCACAACTTTGTGGTATCTTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
* *
2519029 AAGTCCACAGCTCCGTGGCATCATTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
2519056 AAGTCCACAACTCCGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* *
2519083 AAAGTTCACAACTCCATGGCATCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
* * *
2519111 AAAGTCTACAAGTCCATGGCATCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
*
2519139 AAGTCCACAACTCTGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* * *
2519166 AAATCCACAACTCTGTGGCATCCTTTA
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
2519193 AAGTCCACAACTCCGTGGCATTCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* *
2519220 AAGTCCACAACTCCATGGCAT-CATTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
2519246 AAGTCCACAACTCCGTGGCAT-CATTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
2519272 AAGTCCACAACTCCGTGGCATCATTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
2519299 AAAGTCCACAACTCTC-TAGCATCCTTTT
1 -AAGTCCACAACTC-CGTGGCATCCTTTT
* *
2519327 AAGTCCACAACTCTGTGACATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* * **
2519354 AAATTCTACAACTCAATGGCATCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
* *
2519382 AAGTCCATAACTCTGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* * *
2519409 AAGTTCACAACTTCGTGACATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
2519436 AAGTC
1 AAGTC
2519441 TATAATTTTG
Statistics
Matches: 507, Mismatches: 63, Indels: 15
0.87 0.11 0.03
Matches are distributed among these distances:
26 50 0.10
27 259 0.51
28 197 0.39
29 1 0.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCATCCTTTT
Found at i:2519006 original size:55 final size:54
Alignment explanation
Indices: 2518836--2519440 Score: 739
Period size: 55 Copynumber: 11.1 Consensus size: 54
2518826 TTTCTTTTCA
*
2518836 AAGTCCACAACTCCGTGGCATCCTTTTAAAGTTCACAACTCCGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTCCGTGGCATCCTTTT
* * *
2518891 AAAGTTCACAACTCCGTGGCATCCTTTTAAAATCTACAACTCCGTGGCATCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTCCGTGGCATCCTTTT
* * * * *
2518947 AAGTCCACAACTTCATGGCATCCTTTTAAGTCCACAACTTCGTGCCATCATTTT
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTT
** * * * *
2519001 AAAGTCCACAACTTTGTGGTATCTTTTTAAGTCCACAGCTCCGTGGCATCATTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTT
* *
2519056 AAGTCCACAACTCCGTGGCATCCTTTTAAAGTTCACAACTCCATGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTCCGTGGCATCCTTTT
* * * *
2519111 AAAGTCTACAAGTCCATGGCATCCTTTTAAGTCCACAACTCTGTGGCATCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTT
* * * *
2519166 AAATCCACAACTCTGTGGCATCCTTTAAAGTCCACAACTCCGTGGCATTCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTT
* * *
2519220 AAGTCCACAACTCCATGGCAT-CATTTAAGTCCACAACTCCGTGGCAT-CATTT
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTT
* *
2519272 AAGTCCACAACTCCGTGGCATCATTTTAAAGTCCACAACTCTC-TAGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTC-CGTGGCATCCTTTT
* * * * **
2519327 AAGTCCACAACTCTGTGACATCCTTTTAAATTCTACAACTCAATGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTCCGTGGCATCCTTTT
* * * * *
2519382 AAGTCCATAACTCTGTGGCATCCTTTTAAGTTCACAACTTCGTGACATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTT
2519436 AAGTC
1 AAGTC
2519441 TATAATTTTG
Statistics
Matches: 473, Mismatches: 68, Indels: 18
0.85 0.12 0.03
Matches are distributed among these distances:
52 24 0.05
53 27 0.06
54 152 0.32
55 195 0.41
56 75 0.16
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (54 bp):
AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTT
Found at i:2519670 original size:28 final size:28
Alignment explanation
Indices: 2519462--2520452 Score: 859
Period size: 28 Copynumber: 35.2 Consensus size: 28
2519452 GGCATCCTTG
* *
2519462 AAAGCCCACAGAAGTCGGTGGCAACCTTTTT
1 AAAGCCCAC--AAGTCAGTGGC-ACCTTTTC
* * *
2519493 AAAGCCCATAAGTTAGTAGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTC
* * * *
2519522 AAAGCCCATAAGTCTGTGACATC-TTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTC
* *
2519549 AAAGCCTACAAGTTAGTGGCACC-TTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTC
* * *
2519576 AAAGCCCACAAATCATTGTCA-CTTTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTC
* *
2519603 AAAACCCATAAGTCAGTGGCACACTTTTC
1 AAAGCCCACAAGTCAGTGGCAC-CTTTTC
* * * *
2519632 GAAGCCCACAAGTAAATGGCACCTTCTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTC
* *
2519660 AAAGCCCACAAGTTAGTGGCA-CTCGTTC
1 AAAGCCCACAAGTCAGTGGCACCT-TTTC
* * * *
2519688 AAAGCTCATAAGTCAATGGCATC-TTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTC
* *
2519715 AAAGCCCACAAGTCAATGGCATC-TTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTC
* *
2519742 AAAG-CCAGAAAATCAGTGGCACACTTTTC
1 AAAGCCCA-CAAGTCAGTGGCAC-CTTTTC
* *
2519771 AAAGCCGACAAGTAAGTGGCA-CTTTCTC
1 AAAGCCCACAAGTCAGTGGCACCTTT-TC
* *
2519799 AAAGCCCACAAGTTAGTGGCACCCTTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTC
*
2519827 AAAGCCCACAAGTCAGTGACATCC-TTTC
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTC
2519855 AAAGCCCACAAGTCAGTGGCATCC-TTTC
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTC
* * * *
2519883 ACAGCTCATAAGTCAGTGACAACCCTTTTC
1 AAAGCCCACAAGTCAGTGGC-A-CCTTTTC
* *
2519913 AAAGCCCACAAGTCAGTGACACCTTCTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTC
* * * * *
2519941 AAAGCCCATAAGTCAATGGTATCTTTTT
1 AAAGCCCACAAGTCAGTGGCACCTTTTC
*
2519969 AAAGCCCATAAGTCAGTGGCACC-TTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTC
2519996 AAAGCCCACAAGTCAGTGGCA-CTTTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTC
* * ** *
2520023 AAAGCCTACAAGTCAATAACACATTTTTC
1 AAAGCCCACAAGTCAGTGGCAC-CTTTTC
* * *
2520052 AAAGCCCATAAGTAACTGGCACCTTCTT-
1 AAAGCCCACAAGTCAGTGGCACCTT-TTC
* * *
2520080 AAAGCTCACAAGTTAGTGGCATC-TTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTC
* *
2520107 AAAGCCTACAAGTCAGTGGTATCC-TTTC
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTC
* * *
2520135 AAAGCCCACAAATCAGGGGCATCTTTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTC
* * *
2520163 AAAGCTCACAAGTCAGGGGCATCTTTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTC
*
2520191 AAAGCTCACAAGTCAGTGGCAACCCTTTTC
1 AAAGCCCACAAGTCAGTGGC-A-CCTTTTC
*
2520221 AAAGCCCACAAGTCATTGGCAACCCTTTTC
1 AAAGCCCACAAGTCAGTGGC-A-CCTTTTC
*
2520251 AAAGCCCAGAAGTCAGTGGCACCTTCTT-
1 AAAGCCCACAAGTCAGTGGCACCTT-TTC
*
2520279 AAAGCCCACAAGTCTGTGGCATCC-TTTC
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTC
* *
2520307 AAAGCCCACAAGTTAGTGACACCTTTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTC
* * ** * *
2520335 AAAGACCACAAATCAGTATCATCTTTTT
1 AAAGCCCACAAGTCAGTGGCACCTTTTC
* *
2520363 AAAACCCACAAGTCAGTGACACCCTTTT-
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTC
* * *
2520391 AAAGCCCACAAGTAAGTGACATCTTTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTC
* * *
2520419 AAAGCTCATAAGTTAGTGGCATCCTTTT-
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTC
2520447 AAAGCC
1 AAAGCC
2520453 TACATAAGTC
Statistics
Matches: 788, Mismatches: 141, Indels: 65
0.79 0.14 0.07
Matches are distributed among these distances:
26 7 0.01
27 181 0.23
28 396 0.50
29 121 0.15
30 75 0.10
31 8 0.01
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.25
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCACCTTTTC
Found at i:2519723 original size:139 final size:139
Alignment explanation
Indices: 2519462--2520452 Score: 904
Period size: 139 Copynumber: 7.0 Consensus size: 139
2519452 GGCATCCTTG
* * * * * *
2519462 AAAGCCCACAGAAGTCGGTGGCA-ACCTTTTTAAAGCCCATAAGTTAGTAGCACCCTTTTCAAAG
1 AAAGCCCAC--AAGTCAGTGGCACA-CTTTTCAAAGCCCACAAGTAAGTGGCA-CCTTCTCAAAG
* * * * *
2519526 CCCATAAGTCT-GTGACA-TCTTTCAAAGCCTACAAGTTAGTGGCACCTTTCAAAGCCCACAAAT
62 CCCACAAGT-TAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGT
* *
2519589 CATTGTCACTTTTC
126 CAGTGGCACTTTTC
* * * *
2519603 AAAACCCATAAGTCAGTGGCACACTTTTCGAAGCCCACAAGTAAATGGCACCTTCTCAAAGCCCA
1 AAAGCCCACAAGTCAGTGGCACACTTTTCAAAGCCCACAAGTAAGTGGCACCTTCTCAAAGCCCA
* * * * * *
2519668 CAAGTTAGTGGCACTCGTTCAAAGCTCATAAGTCAATGGCATCTTTCAAAGCCCACAAGTCAATG
66 CAAGTTAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTCAGTG
2519733 GCA-TCTTTC
131 GCACT-TTTC
* * * *
2519742 AAAG-CCAGAAAATCAGTGGCACACTTTTCAAAGCCGACAAGTAAGTGGCACTTTCTCAAAGCCC
1 AAAGCCCA-CAAGTCAGTGGCACACTTTTCAAAGCCCACAAGTAAGTGGCACCTTCTCAAAGCCC
* *
2519806 ACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGACATCCTTTCAAAGCCCACAAGTCAG
65 ACAAGTTAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTCAAAGCCCACAAGTCAG
*
2519871 TGGCATCCTTTC
129 TGGCA-CTTTTC
* * * * * * *
2519883 ACAGCTCATAAGTCAGTGACAACCCTTTTCAAAGCCCACAAGTCAGTGACACCTTCTCAAAGCCC
1 AAAGCCCACAAGTCAGTGGC-ACACTTTTCAAAGCCCACAAGTAAGTGGCACCTTCTCAAAGCCC
* * * * * *
2519948 ATAAGTCAATGGTA-TCTTTTTAAAGCCCATAAGTCAGTGGCACCTTTCAAAGCCCACAAGTCAG
65 ACAAGTTAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTCAG
2520012 TGGCACTTTTC
129 TGGCACTTTTC
* * ** * * * * *
2520023 AAAGCCTACAAGTCAATAACACATTTTTCAAAGCCCATAAGTAACTGGCACCTTCTTAAAGCTCA
1 AAAGCCCACAAGTCAGTGGCACACTTTTCAAAGCCCACAAGTAAGTGGCACCTTCTCAAAGCCCA
* * * *
2520088 CAAGTTAGTGGCA-TCTTTCAAAGCCTACAAGTCAGTGGTATCCTTTCAAAGCCCACAAATCAGG
66 CAAGTTAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTCAAAGCCCACAAGTCAGT
2520152 GGCATCTTTTC
130 GGCA-CTTTTC
* * * * * *
2520163 AAAGCTCACAAGTCAGGGGCA-TCTTTTCAAAGCTCACAAGTCAGTGGCAACCCTTTTCAAAGCC
1 AAAGCCCACAAGTCAGTGGCACACTTTTCAAAGCCCACAAGTAAGTGGC-A-CCTTCTCAAAGCC
* * * * *
2520227 CACAAGTCATTGGCAACCCTTTTCAAAGCCCAGAAGTCAGTGGCACCTTCTTAAAGCCCACAAGT
64 CACAAGTTAGTGGC-ACTC-TTTCAAAGCCCACAAGTCAGTGGCACCTT-TCAAAGCCCACAAGT
* *
2520292 CTGTGGCATCCTTTC
126 CAGTGGCA-CTTTTC
* * * * * ** * * * *
2520307 AAAGCCCACAAGTTAGTGACAC-CTTTTCAAAGACCACAAATCAGTATCATCTTTTTAAAACCCA
1 AAAGCCCACAAGTCAGTGGCACACTTTTCAAAGCCCACAAGTAAGTGGCACCTTCTCAAAGCCCA
* * * * * * * * * *
2520371 CAAGTCAGTGACACCCTTTTAAAGCCCACAAGTAAGTGACATCTTTTCAAAGCTCATAAGTTAGT
66 CAAGTTAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTCAAAGCCCACAAGTCAGT
2520436 GGCATCCTTTT-
130 GGCA--CTTTTC
2520447 AAAGCC
1 AAAGCC
2520453 TACATAAGTC
Statistics
Matches: 695, Mismatches: 133, Indels: 45
0.80 0.15 0.05
Matches are distributed among these distances:
137 1 0.00
138 48 0.07
139 263 0.38
140 112 0.16
141 84 0.12
142 96 0.14
143 6 0.01
144 85 0.12
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.25
Consensus pattern (139 bp):
AAAGCCCACAAGTCAGTGGCACACTTTTCAAAGCCCACAAGTAAGTGGCACCTTCTCAAAGCCCA
CAAGTTAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTCAGTG
GCACTTTTC
Found at i:2520859 original size:19 final size:18
Alignment explanation
Indices: 2520802--2520870 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 18
2520792 CATTTTTTTT
*
2520802 AAAAATAATAATAATAATA
1 AAAAATAA-AAAAATAATA
* *
2520821 AAATATAAAAAAGA-GA-A
1 AAAAATAAAAAA-ATAATA
2520838 AAAAATACAAAAAATAATA
1 AAAAATA-AAAAAATAATA
*
2520857 AAAAGTAAAAAAAT
1 AAAAATAAAAAAAT
2520871 TGATGAGTGG
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
17 8 0.20
18 17 0.43
19 15 0.38
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.17
Consensus pattern (18 bp):
AAAAATAAAAAAATAATA
Found at i:2525558 original size:51 final size:51
Alignment explanation
Indices: 2525482--2525582 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 51
2525472 TTATTTATAA
2525482 GGGGATACTCAAACCCTAGTTTTATTTCTAAAACA-CTGATTTTTCACCATC
1 GGGGATACTCAAACCCTAGTTTTATTTCTAAAACATC-GATTTTTCACCATC
*
2525533 GGGGATACTCCAACCCTTA-TTTTATTTCTAAAACATCGATTTTTCACCAT
1 GGGGATACTCAAACCC-TAGTTTTATTTCTAAAACATCGATTTTTCACCAT
2525583 TAGGGATATC
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
51 44 0.94
52 3 0.06
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (51 bp):
GGGGATACTCAAACCCTAGTTTTATTTCTAAAACATCGATTTTTCACCATC
Found at i:2525618 original size:79 final size:79
Alignment explanation
Indices: 2525535--2525991 Score: 401
Period size: 79 Copynumber: 5.8 Consensus size: 79
2525525 TCACCATCGG
* * * * *
2525535 GGATACTCCAACCCTTATTTTATTTCTAAAACATCGATTTTTCACCATTAGGGATA-TCCCAATC
1 GGATACTCCAACCCTGATTTTATTTCTAAAACACCGATTTTTCACCATCAGGGATACT-CTAACC
*
2525599 TTGTTATTTTTGAGA
65 TTGTTATTTTCGAGA
* * * *
2525614 GGATACTTCAAACCTGATTTTATTTCTAAAACACCGATTTTCCACCATCAAGGATACTCTAACCT
1 GGATACTCCAACCCTGATTTTATTTCTAAAACACCGATTTTTCACCATCAGGGATACTCTAACCT
*
2525679 TGTTATTTTCGAGG
66 TGTTATTTTCGAGA
* * * * * *
2525693 GGATGCTTCAACACC-AATTTTATTTCTAAAACACTGATTTTTCGCCATCAGGGATACTCAAACC
1 GGATACTCCAAC-CCTGATTTTATTTCTAAAACACCGATTTTTCACCATCAGGGATACTCTAA-C
*
2525757 CTT-TTA-TTTCGAGG
64 CTTGTTATTTTCGAGA
* * * *
2525771 GGATACTCTAACCCCGATTTTATTTCTAAAATATCGA-TTTTCTACCATC-GAGGATACTCTAAC
1 GGATACTCCAACCCTGATTTTATTTCTAAAACACCGATTTTTC-ACCATCAG-GGATACTCTAAC
* **
2525834 CCTGTTATTTTTAAGA
64 CTTGTTATTTTCGAGA
* ** * * *
2525850 GGAT-CTCTAA-CCTCGATTTTATTTCTGCAACACCGATTTTTCACCATCGGGGGTACTCCAACC
1 GGATACTCCAACCCT-GATTTTATTTCTAAAACACCGATTTTTCACCATCAGGGATACTCTAACC
***
2525913 CCATTATTTTCGAG-
65 TTGTTATTTTCGAGA
* * * * * * * * *
2525927 GGATTACTCCAACTCTGATCTTGTTTCCAAAATATCGACTTTTCATCATCAGGGATACTCCAACC
1 GGA-TACTCCAACCCTGATTTTATTTCTAAAACACCGATTTTTCACCATCAGGGATACTCTAACC
2525992 CTTTTTTTAT
Statistics
Matches: 308, Mismatches: 56, Indels: 28
0.79 0.14 0.07
Matches are distributed among these distances:
77 16 0.05
78 105 0.34
79 178 0.58
80 9 0.03
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (79 bp):
GGATACTCCAACCCTGATTTTATTTCTAAAACACCGATTTTTCACCATCAGGGATACTCTAACCT
TGTTATTTTCGAGA
Found at i:2525660 original size:130 final size:130
Alignment explanation
Indices: 2525422--2525677 Score: 347
Period size: 130 Copynumber: 2.0 Consensus size: 130
2525412 TCATTGATGT
* * *
2525422 TTTTATTTCTAAAATATCGATTTTTCACTATCAGGGATACTCCAACCTCGTTATTTATAAGGGGA
1 TTTTATTTCTAAAACATCGATTTTTCACCATCAGGGATACTCCAACCTCGTTATTTATAAGAGGA
* * **
2525487 TACTCAAACCCTAGTTTTATTTCTAAAACACTGATTTTTCACCATCGGGGATACTCCAACCCTTA
66 TACTCAAACCCTAGTTTTATTTCTAAAACACCGATTTTCCACCATCAAGGATACTCCAACCCTTA
* * * * *
2525552 TTTTATTTCTAAAACATCGATTTTTCACCATTAGGGATA-TCCCAATCTTGTTATTTTTGAGAGG
1 TTTTATTTCTAAAACATCGATTTTTCACCATCAGGGATACT-CCAACCTCGTTATTTATAAGAGG
*
2525616 ATACTTCAAA-CCT-GATTTTATTTCTAAAACACCGATTTTCCACCATCAAGGATACTCTAACC
65 ATAC-TCAAACCCTAG-TTTTATTTCTAAAACACCGATTTTCCACCATCAAGGATACTCCAACC
2525678 TTGTTATTTT
Statistics
Matches: 110, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
129 2 0.02
130 103 0.94
131 5 0.05
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (130 bp):
TTTTATTTCTAAAACATCGATTTTTCACCATCAGGGATACTCCAACCTCGTTATTTATAAGAGGA
TACTCAAACCCTAGTTTTATTTCTAAAACACCGATTTTCCACCATCAAGGATACTCCAACCCTTA
Found at i:2525827 original size:157 final size:155
Alignment explanation
Indices: 2525551--2525993 Score: 443
Period size: 157 Copynumber: 2.8 Consensus size: 155
2525541 TCCAACCCTT
* * *
2525551 ATTTTATTTCTAAAACA-TCGATTTTTCACCATTAGGGATA-TCCCAA-TCTTGTTATTTTTGAG
1 ATTTTATTTCTAAAACACT-GATTTTTCACCATCAGGGATACT-CCAACCCTT-TTATTTTCGAG
* * * *
2525613 AGGATACT-TCAAACCTGATTTTATTTCTAAAACACCGATTTTCCACCATCAAGGATACTCTAAC
63 GGGATACTCT-AACCCTGATTTTATTTCTAAAATATCGATTTT-CACCATC-AGGATACTCTAAC
* * *
2525677 CTTGTTATTTTCGAGGGGATGCT-TCAACAC-CA
125 CCTGTTATTTTCAAGAGGAT-CTCT-AAC-CTCA
* *
2525709 ATTTTATTTCTAAAACACTGATTTTTCGCCATCAGGGATACTCAAACCCTTTTA-TTTCGAGGGG
1 ATTTTATTTCTAAAACACTGATTTTTCACCATCAGGGATACTCCAACCCTTTTATTTTCGAGGGG
*
2525773 ATACTCTAACCCCGATTTTATTTCTAAAATATCGATTTTCTACCATCGAGGATACTCTAACCCTG
66 ATACTCTAACCCTGATTTTATTTCTAAAATATCGATTTTC-ACCATC-AGGATACTCTAACCCTG
* *
2525838 TTATTTTTAAGAGGATCTCTAACCTCG
129 TTATTTTCAAGAGGATCTCTAACCTCA
** * * * **
2525865 ATTTTATTTCTGCAACACCGATTTTTCACCATCGGGGGTACTCCAACCCCATTATTTTCGA-GGG
1 ATTTTATTTCTAAAACACTGATTTTTCACCATCAGGGATACTCCAACCCTTTTATTTTCGAGGGG
* * * * * * *
2525929 ATTACTCCAACTCTGATCTTGTTTCCAAAATATCGACTTTTCATCATCAGGGATACTCCAACCCT
66 A-TACTCTAACCCTGATTTTATTTCTAAAATATCGA-TTTTCACCATCA-GGATACTCTAACCCT
2525994 TTTTTTATTT
Statistics
Matches: 241, Mismatches: 33, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
155 1 0.00
156 57 0.24
157 130 0.54
158 48 0.20
159 5 0.02
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.36
Consensus pattern (155 bp):
ATTTTATTTCTAAAACACTGATTTTTCACCATCAGGGATACTCCAACCCTTTTATTTTCGAGGGG
ATACTCTAACCCTGATTTTATTTCTAAAATATCGATTTTCACCATCAGGATACTCTAACCCTGTT
ATTTTCAAGAGGATCTCTAACCTCA
Found at i:2526050 original size:51 final size:51
Alignment explanation
Indices: 2525931--2526051 Score: 129
Period size: 51 Copynumber: 2.4 Consensus size: 51
2525921 TTCGAGGGAT
* * * * * * *
2525931 TACTCCAACTCTGATCTTGTTTCCAAAATATCGACTTTTCATCATCAGGGA
1 TACTCCAACCCTGTTTTTATTTTCAAAATATCGACTTTTCACCATCAGGAA
* *
2525982 TACTCCAACCCTTTTTTTATTTTCAAAATATCGATTTTTCACCATC-GGTAA
1 TACTCCAACCCTGTTTTTATTTTCAAAATATCGACTTTTCACCATCAGG-AA
2526033 TACTCCAACACC-GTTTTTA
1 TACTCCAAC-CCTGTTTTTA
2526052 GCTCTAAAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
50 2 0.03
51 54 0.93
52 2 0.03
ACGTcount: A:0.27, C:0.26, G:0.08, T:0.39
Consensus pattern (51 bp):
TACTCCAACCCTGTTTTTATTTTCAAAATATCGACTTTTCACCATCAGGAA
Found at i:2526061 original size:51 final size:51
Alignment explanation
Indices: 2525954--2526063 Score: 118
Period size: 51 Copynumber: 2.2 Consensus size: 51
2525944 ATCTTGTTTC
* * * * *
2525954 CAAAATATCGACTTTTCATCATCAGGGATACTCCAACCCTTTTTTTATTTT
1 CAAAATATCGACTTTTCACCATCAGGAATACTCCAACCCTGTTTTTACTCT
*
2526005 CAAAATATCGATTTTTCACCATC-GGTAATACTCCAACACC-GTTTTTAGCTCT
1 CAAAATATCGACTTTTCACCATCAGG-AATACTCCAAC-CCTGTTTTTA-CTCT
2526057 -AAAATAT
1 CAAAATAT
2526064 TAAATTTTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
50 2 0.04
51 44 0.88
52 4 0.08
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.37
Consensus pattern (51 bp):
CAAAATATCGACTTTTCACCATCAGGAATACTCCAACCCTGTTTTTACTCT
Found at i:2527661 original size:19 final size:19
Alignment explanation
Indices: 2527637--2527673 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2527627 TTATAAGCAC
2527637 TAAACATAATTAAAAACAT
1 TAAACATAATTAAAAACAT
* *
2527656 TAAACATAGTTATAAACA
1 TAAACATAATTAAAAACA
2527674 CAAGCACAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.11, G:0.03, T:0.27
Consensus pattern (19 bp):
TAAACATAATTAAAAACAT
Found at i:2531706 original size:56 final size:56
Alignment explanation
Indices: 2531580--2531707 Score: 159
Period size: 56 Copynumber: 2.3 Consensus size: 56
2531570 TACTTTCTAA
* * * *
2531580 GCTGTTG-CTGTTGCTATTAATTTGATTTAATCTTCAATCTGGGTTTGGTTTTTTT
1 GCTGTTGCCTGTTGCTATTAATTCGATCTAATCTTCAACCTGGGTTTGGTTTTATT
* * * *
2531635 GCTATTGCTTGTTGCTATTAATTCGGTCTAATCTTCTACCTGGGTTTGGTTTTATT
1 GCTGTTGCCTGTTGCTATTAATTCGATCTAATCTTCAACCTGGGTTTGGTTTTATT
* *
2531691 GTTGTTGCCTATTGCTA
1 GCTGTTGCCTGTTGCTA
2531708 CCTGATTATA
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
55 6 0.10
56 54 0.90
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (56 bp):
GCTGTTGCCTGTTGCTATTAATTCGATCTAATCTTCAACCTGGGTTTGGTTTTATT
Found at i:2531881 original size:12 final size:12
Alignment explanation
Indices: 2531864--2531898 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
2531854 TTTTTTTAAG
2531864 TTAAATATTTTA
1 TTAAATATTTTA
*
2531876 TTAAATATATT-
1 TTAAATATTTTA
2531887 TTAAATATTTTA
1 TTAAATATTTTA
2531899 AATATTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTAAATATTTTA
Found at i:2531894 original size:9 final size:9
Alignment explanation
Indices: 2531882--2531913 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
2531872 TTTATTAAAT
2531882 ATATTTTAA
1 ATATTTTAA
2531891 ATATTTTAA
1 ATATTTTAA
2531900 ATATTTTAA
1 ATATTTTAA
2531909 ATATT
1 ATATT
2531914 ATTTCGGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATATTTTAA
Found at i:2531982 original size:17 final size:17
Alignment explanation
Indices: 2531960--2531995 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2531950 AATAACAGAA
2531960 AACCGATGAAATTGATT
1 AACCGATGAAATTGATT
2531977 AACCGATGAAATTGATT
1 AACCGATGAAATTGATT
2531994 AA
1 AA
2531996 TAACAGACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (17 bp):
AACCGATGAAATTGATT
Found at i:2534059 original size:56 final size:56
Alignment explanation
Indices: 2533945--2534061 Score: 189
Period size: 56 Copynumber: 2.1 Consensus size: 56
2533935 GCTATTGTTG
* *
2533945 TTGCTATTAATTTGATCTAATCTTCAATCTGGGTTTGGTTTTGTTGCTATTACTTA
1 TTGCTATTAATTTGATCTAATCTTCAATCTGGCTTTGGTTTTGTTGCTATTACCTA
* * *
2534001 TTGCTATTAATTTGGTCTAATCTTCAATCTGGCTTTGGTTTTGTTGCTGTTGCCTA
1 TTGCTATTAATTTGATCTAATCTTCAATCTGGCTTTGGTTTTGTTGCTATTACCTA
2534057 TTGCT
1 TTGCT
2534062 GCCTGATTGT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.16, C:0.15, G:0.18, T:0.51
Consensus pattern (56 bp):
TTGCTATTAATTTGATCTAATCTTCAATCTGGCTTTGGTTTTGTTGCTATTACCTA
Found at i:2534283 original size:22 final size:23
Alignment explanation
Indices: 2534227--2534274 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
2534217 TCAAATGGGT
2534227 TTTTAAATATTTTATTATATATA
1 TTTTAAATATTTTATTATATATA
2534250 TTTTAAATATTTTA-TATAT-TA
1 TTTTAAATATTTTATTATATATA
2534271 TTTT
1 TTTT
2534275 GATTAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 6 0.24
22 5 0.20
23 14 0.56
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTAAATATTTTATTATATATA
Found at i:2540025 original size:13 final size:13
Alignment explanation
Indices: 2540007--2540045 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2539997 ATAATCCTCC
*
2540007 TGTATCGATACAG
1 TGTATCGATACAA
2540020 TGTATCGATACAA
1 TGTATCGATACAA
2540033 TGTATCGATACAA
1 TGTATCGATACAA
2540046 AGAATTATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2546222 original size:19 final size:20
Alignment explanation
Indices: 2546179--2546229 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
2546169 TACAAGCTAA
* **
2546179 TGTATCAATACATTTTATGG
1 TGTATCGATACATACTATGG
2546199 TGTATCGATACATACTAT-G
1 TGTATCGATACATACTATGG
2546218 TGTATCGATACA
1 TGTATCGATACA
2546230 AGTTTAGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATACTATGG
Found at i:2552030 original size:19 final size:20
Alignment explanation
Indices: 2551968--2552051 Score: 77
Period size: 20 Copynumber: 4.2 Consensus size: 20
2551958 ACCCTAAAAA
*
2551968 GTATCGATACATA-TCCAAAT
1 GTATCGATACATACT-CAATT
* *
2551988 GTATCAATACATTA-TGC-TTT
1 GTATCGATACA-TACT-CAATT
*
2552008 GTATCGATACATGCTC-ATT
1 GTATCGATACATACTCAATT
2552027 GTATCGATACATACTCAATT
1 GTATCGATACATACTCAATT
2552047 GTATC
1 GTATC
2552052 AATATATGAA
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
19 19 0.36
20 30 0.57
21 4 0.08
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (20 bp):
GTATCGATACATACTCAATT
Found at i:2553753 original size:24 final size:24
Alignment explanation
Indices: 2553709--2553754 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2553699 ACCATCAAAG
*
2553709 ATGATGAAGATGATGATGATAATA
1 ATGATGAAGATGATCATGATAATA
*
2553733 ATGATGAAGTTGACTCA-GATAA
1 ATGATGAAGATGA-TCATGATAA
2553755 ACAAATGGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.43, C:0.04, G:0.24, T:0.28
Consensus pattern (24 bp):
ATGATGAAGATGATCATGATAATA
Found at i:2560828 original size:13 final size:13
Alignment explanation
Indices: 2560810--2560835 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2560800 CATATCCAGA
2560810 TGTATCGATACAT
1 TGTATCGATACAT
2560823 TGTATCGATACAT
1 TGTATCGATACAT
2560836 ACTCAATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2560833 original size:33 final size:32
Alignment explanation
Indices: 2560791--2560854 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
2560781 ACCCTAGAAA
2560791 GTATCGATACATA-TCCAGATGTATCGATACATT
1 GTATCGATACATACT-CA-ATGTATCGATACATT
*
2560824 GTATCGATACATACTCAATTTATCGATACAT
1 GTATCGATACATACTCAATGTATCGATACAT
2560855 GAAACTGGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.45
33 15 0.52
34 1 0.03
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (32 bp):
GTATCGATACATACTCAATGTATCGATACATT
Found at i:2560909 original size:20 final size:20
Alignment explanation
Indices: 2560884--2560936 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
2560874 CTAAGTGAAA
*
2560884 TGTATCGATACATG-GGACAT
1 TGTATCGATACATGAAGA-AT
*
2560904 TGTATCGATACGTGAAGAAT
1 TGTATCGATACATGAAGAAT
*
2560924 TGTATCAATACAT
1 TGTATCGATACAT
2560937 TATACCTAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATGAAGAAT
Found at i:2563144 original size:13 final size:13
Alignment explanation
Indices: 2563126--2563150 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2563116 TTGAAAAAAG
2563126 AAAATTTAATAAC
1 AAAATTTAATAAC
2563139 AAAATTTAATAA
1 AAAATTTAATAA
2563151 AATTAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATTTAATAAC
Found at i:2563189 original size:27 final size:26
Alignment explanation
Indices: 2563147--2563215 Score: 70
Period size: 27 Copynumber: 2.7 Consensus size: 26
2563137 ACAAAATTTA
*
2563147 ATAAAATTAAAA--TAAAATTAAAAGT
1 ATAAAAATAAAATTTAAAATTAAAA-T
** *
2563172 ATAATGATAAAATTTAAAAATTTAAAT
1 ATAAAAATAAAATTT-AAAATTAAAAT
2563199 ATAAAAATAAAATTTAA
1 ATAAAAATAAAATTTAA
2563216 GAATAGCTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
25 9 0.26
26 2 0.06
27 15 0.43
28 9 0.26
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (26 bp):
ATAAAAATAAAATTTAAAATTAAAAT
Found at i:2563202 original size:21 final size:21
Alignment explanation
Indices: 2563126--2563220 Score: 74
Period size: 21 Copynumber: 4.7 Consensus size: 21
2563116 TTGAAAAAAG
*
2563126 AAAATTTAATAACAAAATTTA
1 AAAATTTAATAATAAAATTTA
*
2563147 ATAAAATTAA-AATAAAA-TTA
1 A-AAATTTAATAATAAAATTTA
* * *
2563167 AAAGTATAATGATAAAATTTA
1 AAAATTTAATAATAAAATTTA
*
2563188 AAAATTTAA-ATATAAAA-AT-
1 AAAATTTAATA-ATAAAATTTA
*
2563207 AAAATTTAAGAATA
1 AAAATTTAATAATA
2563221 GCTCATAATA
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
19 17 0.29
20 12 0.20
21 23 0.39
22 7 0.12
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (21 bp):
AAAATTTAATAATAAAATTTA
Found at i:2563282 original size:8 final size:8
Alignment explanation
Indices: 2563269--2563299 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
2563259 GCCCATAATG
2563269 TAATATAA
1 TAATATAA
2563277 TAATATAA
1 TAATATAA
2563285 TAATATAA
1 TAATATAA
2563293 TAATATA
1 TAATATA
2563300 TTAAAATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
TAATATAA
Found at i:2563686 original size:15 final size:15
Alignment explanation
Indices: 2563644--2563702 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
2563634 GTTTGTATTA
2563644 TTTTAATTTTAAATTAT
1 TTTTAA-TTTAAATT-T
* *
2563661 TTTAAACTTAAATTT
1 TTTTAATTTAAATTT
* *
2563676 TTTTAATTTAAACTA
1 TTTTAATTTAAATTT
2563691 TTTTATATTTAA
1 TTTTA-ATTTAA
2563703 GTCATTTGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
15 17 0.49
16 13 0.37
17 5 0.14
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTAATTTAAATTT
Found at i:2563701 original size:16 final size:15
Alignment explanation
Indices: 2563640--2563702 Score: 72
Period size: 16 Copynumber: 4.0 Consensus size: 15
2563630 TTGAGTTTGT
2563640 ATTATTTTAATTTTAA
1 ATTATTTTAA-TTTAA
*
2563656 ATTATTTTAAACTTAA
1 ATTATTTT-AATTTAA
*
2563672 ATTTTTTTAATTTAA
1 ATTATTTTAATTTAA
*
2563687 ACTATTTTATATTTAA
1 ATTATTTTA-ATTTAA
2563703 GTCATTTGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
15 13 0.32
16 25 0.62
17 2 0.05
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTATTTTAATTTAA
Found at i:2565965 original size:31 final size:32
Alignment explanation
Indices: 2565930--2566005 Score: 77
Period size: 31 Copynumber: 2.4 Consensus size: 32
2565920 TCCATGTAAA
* *
2565930 ATTTAATTAAATATAATAATTTTC-AATAATT
1 ATTTAATTAAATAGAATAATTATCAAATAATT
* *
2565961 ATTT-ATTTACTAAGAATAATTATCAAATAATT
1 ATTTAATTAAAT-AGAATAATTATCAAATAATT
2565993 ATTTTAA-TAAATA
1 A-TTTAATTAAATA
2566006 AGAACAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
30 5 0.14
31 14 0.40
32 9 0.26
33 6 0.17
34 1 0.03
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (32 bp):
ATTTAATTAAATAGAATAATTATCAAATAATT
Found at i:2580173 original size:23 final size:24
Alignment explanation
Indices: 2580143--2580195 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
2580133 TCATCAGTGA
2580143 TCCACTCTAAC-GCGAAAGATATC
1 TCCACTCTAACGGCGAAAGATATC
2580166 TCCACTCTAACGGCGAAAGATATC
1 TCCACTCTAACGGCGAAAGATATC
2580190 TCCACT
1 TCCACT
2580196 GTGATAGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 11 0.38
24 18 0.62
ACGTcount: A:0.32, C:0.32, G:0.13, T:0.23
Consensus pattern (24 bp):
TCCACTCTAACGGCGAAAGATATC
Found at i:2580975 original size:68 final size:69
Alignment explanation
Indices: 2580891--2581028 Score: 260
Period size: 68 Copynumber: 2.0 Consensus size: 69
2580881 CCTGTAAGCA
2580891 TTGCAACTGCAAGAAGTCAAAGTGCTTGAATTTTTAATCAAAAACTCTGACGTTA-CTATCTTCT
1 TTGCAACTGCAAGAAGTCAAAGTGCTTGAATTTTTAATCAAAAACTCTGACGTTACCTATCTTCT
2580955 AGTT
66 AGTT
2580959 TTGCAACTGCAAGAAGTCAAAGTGCTTGAATTTTTAATCAAAAACTCTGACGTTACTCTATCTTC
1 TTGCAACTGCAAGAAGTCAAAGTGCTTGAATTTTTAATCAAAAACTCTGACGTTAC-CTATCTTC
2581024 TAGTT
65 TAGTT
2581029 CGTCAATTTG
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
68 55 0.81
70 13 0.19
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (69 bp):
TTGCAACTGCAAGAAGTCAAAGTGCTTGAATTTTTAATCAAAAACTCTGACGTTACCTATCTTCT
AGTT
Found at i:2581194 original size:43 final size:43
Alignment explanation
Indices: 2581133--2581217 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
2581123 TTTCATCAAA
2581133 GAGCAAACTAGCTTTATCTTTTATATATCGCCAGTGGATCATT
1 GAGCAAACTAGCTTTATCTTTTATATATCGCCAGTGGATCATT
2581176 GAGCAAACTAGCTTTATCTTTTATATATCGCCAGTGGATCAT
1 GAGCAAACTAGCTTTATCTTTTATATATCGCCAGTGGATCAT
2581218 CAGTGGATCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.36
Consensus pattern (43 bp):
GAGCAAACTAGCTTTATCTTTTATATATCGCCAGTGGATCATT
Found at i:2583295 original size:2 final size:2
Alignment explanation
Indices: 2583290--2583314 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2583280 CTTTTTTTTA
2583290 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2583315 CCCCCACCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2586890 original size:21 final size:21
Alignment explanation
Indices: 2586866--2586905 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2586856 ATGTTTTATT
2586866 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TATAAAATATA
2586887 TAAATATTAATATAAAATA
1 TAAATATTAATATAAAATA
2586906 ATTATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:2586917 original size:32 final size:33
Alignment explanation
Indices: 2586836--2586917 Score: 78
Period size: 33 Copynumber: 2.5 Consensus size: 33
2586826 AGTTTATTTT
* * * *
2586836 AAATTATTATTTAATA-ATAAATGTTTTATTTA
1 AAATAATTATTTAATATATAAATGATTAATATA
* **
2586868 AATTTAATTATAAAATATATAAAT-ATTAATATA
1 AA-ATAATTATTTAATATATAAATGATTAATATA
2586901 AAATAATTATTTAATAT
1 AAATAATTATTTAATAT
2586918 TTAATTTTTT
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
32 14 0.37
33 18 0.47
34 6 0.16
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (33 bp):
AAATAATTATTTAATATATAAATGATTAATATA
Found at i:2588492 original size:18 final size:18
Alignment explanation
Indices: 2588447--2588507 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
2588437 TAATTCATAT
* *
2588447 TTTATAAATTTTGATATA
1 TTTATATATTTTGTTATA
*
2588465 TTTGTATATTTTGTTATA
1 TTTATATATTTTGTTATA
*
2588483 TTTATTTATTTT-TTATTA
1 TTTATATATTTTGTTA-TA
2588501 TTT-TATA
1 TTTATATA
2588508 CTTTAATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
17 6 0.17
18 30 0.83
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (18 bp):
TTTATATATTTTGTTATA
Found at i:2588872 original size:3 final size:3
Alignment explanation
Indices: 2588864--2588895 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2588854 AACAAAAAGC
2588864 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2588896 AAAGATAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2588916 original size:7 final size:7
Alignment explanation
Indices: 2588891--2588924 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
2588881 TAATAATAAT
2588891 AATAAAA
1 AATAAAA
*
2588898 AGATAAAG
1 A-ATAAAA
2588906 AATAAAA
1 AATAAAA
2588913 AATAAAA
1 AATAAAA
2588920 AATAA
1 AATAA
2588925 TTTAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (7 bp):
AATAAAA
Found at i:2588976 original size:22 final size:23
Alignment explanation
Indices: 2588943--2588993 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
2588933 TAATTTAATT
2588943 AATT-TATGTAATATTTTTA-AA
1 AATTATATGTAATATTTTTATAA
* * *
2588964 AATTATATTTAATTTTTTTATTA
1 AATTATATGTAATATTTTTATAA
2588987 AATTATA
1 AATTATA
2588994 ATAGTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 4 0.16
22 13 0.52
23 8 0.32
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
AATTATATGTAATATTTTTATAA
Found at i:2589345 original size:22 final size:22
Alignment explanation
Indices: 2589320--2589381 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
2589310 TATGTTTTTT
2589320 ATTATTAATAAAATTTATTAAA
1 ATTATTAATAAAATTTATTAAA
* *
2589342 ATTA-AAAGTAAAATTT-TTAAT
1 ATTATTAA-TAAAATTTATTAAA
*
2589363 TTTATTAA-ATAAATTTATT
1 ATTATTAATA-AAATTTATT
2589382 TGATCATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
20 1 0.03
21 15 0.47
22 16 0.50
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTATTAATAAAATTTATTAAA
Found at i:2601728 original size:19 final size:19
Alignment explanation
Indices: 2601696--2601758 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
2601686 TAAAGTGTAC
*
2601696 AGTAACCATATACGTGAAT
1 AGTACCCATATACGTGAAT
* * *
2601715 AGTGCCCGTATACGTAAAT
1 AGTACCCATATACGTGAAT
*
2601734 AGTACCTATATACGTGAAT
1 AGTACCCATATACGTGAAT
2601753 AGTACC
1 AGTACC
2601759 TCGACAACCA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (19 bp):
AGTACCCATATACGTGAAT
Found at i:2602062 original size:50 final size:50
Alignment explanation
Indices: 2602002--2602160 Score: 248
Period size: 50 Copynumber: 3.2 Consensus size: 50
2601992 TATACTTAGA
*
2602002 GTCAATAATTATGGCCACCTC-CTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTC-TCTATTGTCAAAGGTTGGTGAAGAATC
* * *
2602052 GTCAACAATTATGGCCATCTCTCTCTATTGTTAAAAGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
2602102 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGGATA
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
2602152 GTCAACAAT
1 GTCAACAAT
2602161 GGCAACAACT
Statistics
Matches: 99, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
50 98 0.99
51 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:2604321 original size:15 final size:15
Alignment explanation
Indices: 2604301--2604330 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2604291 GATGTGTTGA
2604301 ACTTCAATCTATTTT
1 ACTTCAATCTATTTT
2604316 ACTTCAATCTATTTT
1 ACTTCAATCTATTTT
2604331 GCTTACATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.53
Consensus pattern (15 bp):
ACTTCAATCTATTTT
Found at i:2606172 original size:46 final size:46
Alignment explanation
Indices: 2606105--2606195 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
2606095 ATTATCAAAG
* *
2606105 ATTGGTGAAGAATAATCAACAATTACAACCACCTCTCTCGATTGTC
1 ATTGGTGAAAAATAATAAACAATTACAACCACCTCTCTCGATTGTC
* * * *
2606151 ATTGGTGAAAAATAGTAAACAATTACGATCACCTCTCTTGATTGT
1 ATTGGTGAAAAATAATAAACAATTACAACCACCTCTCTCGATTGT
2606196 TAAAAGTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (46 bp):
ATTGGTGAAAAATAATAAACAATTACAACCACCTCTCTCGATTGTC
Found at i:2607567 original size:17 final size:18
Alignment explanation
Indices: 2607545--2607578 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2607535 TTTATTAACA
2607545 ATTTTA-AAAAAATTATT
1 ATTTTATAAAAAATTATT
2607562 ATTTTATAAAAAATTAT
1 ATTTTATAAAAAATTAT
2607579 AAAGTATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTTATAAAAAATTATT
Found at i:2607634 original size:18 final size:19
Alignment explanation
Indices: 2607592--2607640 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
2607582 GTATGCATTG
2607592 ATATTTATTAATATAATTC
1 ATATTTATTAATATAATTC
*
2607611 AAATTTATTAATAT-ATTC
1 ATATTTATTAATATAATTC
*
2607629 ATATTTAATAAT
1 ATATTTATTAAT
2607641 CGTATAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATTTATTAATATAATTC
Found at i:2608506 original size:13 final size:13
Alignment explanation
Indices: 2608490--2608527 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
2608480 AATGAAATTG
2608490 ATTAAAGAAAAAA
1 ATTAAAGAAAAAA
2608503 ATTAAA-AAAAAA
1 ATTAAAGAAAAAA
*
2608515 A-GAAAGAAAAAA
1 ATTAAAGAAAAAA
2608527 A
1 A
2608528 AATAAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 3 0.13
12 14 0.61
13 6 0.26
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.11
Consensus pattern (13 bp):
ATTAAAGAAAAAA
Found at i:2608518 original size:20 final size:20
Alignment explanation
Indices: 2608493--2608538 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
2608483 GAAATTGATT
2608493 AAAGAAA-AAAATTAAAAA-AA
1 AAAGAAAGAAAA--AAAAATAA
2608513 AAAGAAAGAAAAAAAAATAA
1 AAAGAAAGAAAAAAAAATAA
2608533 AAAGAA
1 AAAGAA
2608539 TATGTAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.21
20 15 0.62
21 4 0.17
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.07
Consensus pattern (20 bp):
AAAGAAAGAAAAAAAAATAA
Found at i:2608527 original size:16 final size:16
Alignment explanation
Indices: 2608506--2608538 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2608496 GAAAAAAATT
*
2608506 AAAAAAAAA-AGAAAG
1 AAAAAAAAATAAAAAG
2608521 AAAAAAAAATAAAAAG
1 AAAAAAAAATAAAAAG
2608537 AA
1 AA
2608539 TATGTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (16 bp):
AAAAAAAAATAAAAAG
Found at i:2608726 original size:25 final size:24
Alignment explanation
Indices: 2608688--2608735 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
2608678 AAAAATATAA
*
2608688 TCATTTTTATTTTTATATCTATTTT
1 TCATTTTTATTTTTA-ATCAATTTT
2608713 TCATTTTT-TGTTTTAATCAATTT
1 TCATTTTTAT-TTTTAATCAATTT
2608736 CTATATCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.21, C:0.08, G:0.02, T:0.69
Consensus pattern (24 bp):
TCATTTTTATTTTTAATCAATTTT
Found at i:2608826 original size:22 final size:23
Alignment explanation
Indices: 2608779--2608838 Score: 88
Period size: 22 Copynumber: 2.6 Consensus size: 23
2608769 TAATTTATTT
2608779 TTAAATAAAAATAATATAATATA
1 TTAAATAAAAATAATATAATATA
2608802 TTAATATAAAAATAATAT-ATA-A
1 TTAA-ATAAAAATAATATAATATA
2608824 TTAAATTAAAAATAA
1 TTAAA-TAAAAATAA
2608839 GTTTAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
21 1 0.03
22 14 0.40
23 7 0.20
24 13 0.37
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
TTAAATAAAAATAATATAATATA
Found at i:2614435 original size:42 final size:42
Alignment explanation
Indices: 2614371--2614489 Score: 166
Period size: 42 Copynumber: 2.8 Consensus size: 42
2614361 TAGCCCTCAA
* * *
2614371 AGAGAAAGAAGAGAGAGAAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
2614413 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* * * *
2614455 AGAGATAATAAAGAGAGGAGGGGTGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
2614490 GAGAGAAGAA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.44, C:0.03, G:0.45, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:2619138 original size:20 final size:20
Alignment explanation
Indices: 2619091--2619165 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
2619081 AAAAGGACAT
*
2619091 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
2619110 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
2619131 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
2619151 AATGTATCGATACAT
1 AATGTATCGATACAT
2619166 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:2619159 original size:40 final size:39
Alignment explanation
Indices: 2619088--2619165 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
2619078 GGTAAAAGGA
* *
2619088 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
2619127 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
2619166 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:2619820 original size:86 final size:86
Alignment explanation
Indices: 2619660--2621164 Score: 2109
Period size: 86 Copynumber: 17.5 Consensus size: 86
2619650 GGGTTACCAT
* * * * *
2619660 TGACTTGCATGGGCTTTAAAAGGGTGCCACTGACGTGCGTGGGCTTTG-AAAGAATGCCACTAAC
1 TGACTTG--TGGGCTTTGAAAGAGTGCCACTGAC-T-TGTGGGCTTTGAAAAGAGTGCCACTGAC
*
2619724 TCGTGGGCTTTGAAAGGA-TGCCAC
62 TTGTGGGCTTTGAAAGGAGTGCCAC
*
2619748 TGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTACCACTGACTTGC
1 TGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTT--
* *
2619812 GTGAGCTTTAAAAGGAGTGCCAC
64 GTGGGCTTTGAAAGGAGTGCCAC
* * *
2619835 TGACTTGTGTGAGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGAATT
1 TGACTTGTG-G-GCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTT
* * * *
2619899 GTGGGCTTCGCAATG-GTGCCAT
64 GTGGGCTTTGAAAGGAGTGCCAC
* * * * *
2619921 TGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTCTG-AAAGGGTGCCACTAACTTGT
1 TGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGT
*
2619985 GGGCTTTGAAAGG-GTGCCAT
66 GGGCTTTGAAAGGAGTGCCAC
* *
2620005 TGACTTGTGGGCTTTGAAAAGAGCGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
1 TGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
2620070 TGGGCTTTGAAAGGAGTGCCAC
65 TGGGCTTTGAAAGGAGTGCCAC
* * * * *
2620092 TGACTTGTGGGCTTTGAAAGGGTGCCATTGACTTGTGGTCTTTGAAAAGAGTGCTACTGATTTGT
1 TGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGT
*
2620157 GGGCTTTGAAAAGAGTGCCAC
66 GGGCTTTGAAAGGAGTGCCAC
* * *
2620178 TGACTTGTGGACTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTG
1 TGACTTGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
2620242 TGGGCTTTGAAAGGAGTGCCAC
65 TGGGCTTTGAAAGGAGTGCCAC
* * *
2620264 TGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCTACTGACTTGT
1 TGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGT
2620329 GGGCTTTGAAAGG-GTGCCAC
66 GGGCTTTGAAAGGAGTGCCAC
* * *
2620349 TGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGT
1 TGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGT
*
2620414 GGGCTTTGAAAAGAGTGCCAC
66 GGGCTTTGAAAGGAGTGCCAC
* * *
2620435 TGACTTGTGGGCTTTGAAAGGAGTGCCACTAACTTGTGGGCTTTG-AAAGGGTACCACTGACTTG
1 TGACTTGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
*
2620499 TGGGCTTTGAAAAGAGTGCCAC
65 TGGGCTTTGAAAGGAGTGCCAC
*
2620521 TGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTG
1 TGACTTGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
2620586 TGGGCTTTGAAAGG-GTGCCAC
65 TGGGCTTTGAAAGGAGTGCCAC
*
2620607 TAACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACTTG
1 TGACTTGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
*
2620671 TGGGCTTTGAAAAGAGTGCCAC
65 TGGGCTTTGAAAGGAGTGCCAC
* * * *
2620693 TGACTTGTGGGCTTTGAAAGGAGTGCCACTAACTTGTGGGCTTTG-AAAGGGTACCACTAACTTG
1 TGACTTGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
*
2620757 TGAGCTTTGAAAGGAGTGCCAC
65 TGGGCTTTGAAAGGAGTGCCAC
* *
2620779 TGACTTGTGGGCTTTGAAA-AGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTA
1 TGACTTGTGGGCTTTGAAAGA-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
*
2620843 TGGGCTTTGAAAAGAGTGCCAC
65 TGGGCTTTGAAAGGAGTGCCAC
* * *
2620865 TGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGAGTTG
1 TGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
2620930 TGGGCTTTGAAAGG-GTGCCAC
65 TGGGCTTTGAAAGGAGTGCCAC
*
2620951 TGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
1 TGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
2621016 TGGGCTTTGAAAGGAGTGCCAC
65 TGGGCTTTGAAAGGAGTGCCAC
* * *
2621038 TGACTTGTGGG----AAAAG-GTGCCACTGACTTGT-GGCTTTG-AAAGGGTGTCACTGACTTGT
1 TGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGT
*
2621096 GGGCTTTGAAAAGAGTGCCAC
66 GGGCTTTGAAAGGAGTGCCAC
* *
2621117 TGATTTGTGGGCTTTAAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
1 TGACTTGTGGGCTTT-GAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
2621165 GGGATGAACA
Statistics
Matches: 1285, Mismatches: 102, Indels: 61
0.89 0.07 0.04
Matches are distributed among these distances:
79 48 0.04
80 7 0.01
81 14 0.01
82 4 0.00
84 105 0.08
85 203 0.16
86 651 0.51
87 197 0.15
88 13 0.01
89 43 0.03
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.29
Consensus pattern (86 bp):
TGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGT
GGGCTTTGAAAGGAGTGCCAC
Found at i:2620041 original size:29 final size:29
Alignment explanation
Indices: 2619642--2621164 Score: 2091
Period size: 29 Copynumber: 53.2 Consensus size: 29
2619632 ACAGTGGTGA
* * *
2619642 TTTGAAAAGGGTTACCATTGACTTGCATGGGC
1 TTTGAAAAGAG-TGCCACTGACTTG--TGGGC
* *
2619674 TTT-AAAAGGGTGCCACTGACGTGCGTGGGC
1 TTTGAAAAGAGTGCCACTGAC-T-TGTGGGC
* * *
2619704 TTTG-AAAGAATGCCACTAACTCGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2619732 TTTGAAAGGA-TGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
2619760 TTTG-AAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2619788 TTTGAAAAG-GTACCACTGACTTGCGTGAGC
1 TTTGAAAAGAGTGCCACTGACTT--GTGGGC
2619818 TTT-AAAAGGAGTGCCACTGACTTGTGTGAGC
1 TTTGAAAA-GAGTGCCACTGACTTGTG-G-GC
*
2619849 TTT-AAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2619877 TTTG-AAAGAGTGCCACTGAATTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * * *
2619905 TTCGCAATG-GTGCCATTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2619933 TTCG-AAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
2619961 TCTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2619989 TTTG-AAAGGGTGCCATTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2620017 TTTGAAAAGAGCGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
2620046 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2620075 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
2620104 TTTG-AAAGGGTGCCATTGACTTGTGGTC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2620132 TTTGAAAAGAGTGCTACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2620161 TTTGAAAAGAGTGCCACTGACTTGTGGAC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2620190 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2620219 TTTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2620247 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2620276 TTTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2620304 TTTGAAAAGAGTGCTACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2620333 TTTG-AAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2620361 TTTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2620389 TTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
2620418 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2620447 TTTGAAAGGAGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2620476 TTTG-AAAGGGTACCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
2620504 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2620533 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2620562 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2620591 TTTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2620619 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
2620648 TTTGAAAAG-GTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
2620676 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2620705 TTTGAAAGGAGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * * *
2620734 TTTG-AAAGGGTACCACTAACTTGTGAGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2620762 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
2620791 TTTGAAAAG-GTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2620819 TTTGAAAAGAGTGCCACTAACTTATGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2620848 TTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
2620877 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2620906 TTTGAAAGGAGTGCCACTGAGTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2620935 TTTG-AAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2620963 TTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
2620992 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2621021 TTTGAAAGGAGTGCCACTGACTTGT-GG-
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
2621048 ---GAAAAG-GTGCCACTGACTTGT-GGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2621072 TTTG-AAAGGGTGTCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2621100 TTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2621129 TTTAAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
2621158 TTTGAAA
1 TTTGAAA
2621165 GGGATGAACA
Statistics
Matches: 1338, Mismatches: 120, Indels: 69
0.88 0.08 0.05
Matches are distributed among these distances:
23 17 0.01
24 5 0.00
26 4 0.00
27 22 0.02
28 478 0.36
29 724 0.54
30 55 0.04
31 29 0.02
32 4 0.00
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.29
Consensus pattern (29 bp):
TTTGAAAAGAGTGCCACTGACTTGTGGGC
Found at i:2620112 original size:115 final size:115
Alignment explanation
Indices: 2619642--2621164 Score: 2113
Period size: 115 Copynumber: 13.3 Consensus size: 115
2619632 ACAGTGGTGA
* * * *
2619642 TTTGAAAAGGGTTACCATTGACTTGCATGGGCTTT-AAAAGGGTGCCACTGACGTGCGTGGGCTT
1 TTTG-AAAGGG-TGCCACTGACTTG--TGGGCTTTGAAAAGAGTGCCACTGAC-T-TGTGGGCTT
* * *
2619706 TG-AAAGAATGCCACTAACTCGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGC
60 TGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* * *
2619760 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTACCACTGACTTGCGTGAGCTTT-AA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTT--GTGGGCTTTGAA
*
2619823 AAGGAGTGCCACTGACTTGTGTGAGCTTTAAAAGG-GTGCCACTGACTTGTGGGC
64 AA-GAGTGCCACTGACTTGTG-G-GCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* * * * * * *
2619877 TTTGAAAGAGTGCCACTGAATTGTGGGCTTCGCAATG-GTGCCATTGACTTGTGGGCTTCG-AAA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA
* * *
2619940 GGGTGCCACTGACTTGTGGGCTCTGAAAGG-GTGCCACTAACTTGTGGGC
66 GAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* * *
2619989 TTTGAAAGGGTGCCATTGACTTGTGGGCTTTGAAAAGAGCGCCACTGATTTGTGGGCTTTGAAAA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA
2620054 GAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
66 GAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* * * *
2620104 TTTGAAAGGGTGCCATTGACTTGTGGTCTTTGAAAAGAGTGCTACTGATTTGTGGGCTTTGAAAA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA
*
2620169 GAGTGCCACTGACTTGTGGACTTTGAAAGGAGTGCCACTGACTTGTGGGC
66 GAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* *
2620219 TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AAA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA
* * * *
2620283 GGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCTACTGACTTGTGGGC
66 GAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* *
2620333 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTGAAAA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA
* *
2620397 GAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
66 GAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* * *
2620447 TTTGAAAGGAGTGCCACTAACTTGTGGGCTTTG-AAAGGGTACCACTGACTTGTGGGCTTTGAAA
1 TTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
2620511 AGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
65 AGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* *
2620562 TTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTGAAA
1 TTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
* *
2620626 GGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGC
65 AGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* * *
2620676 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTAACTTGTGGGCTTTG-AA
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
* * * *
2620740 AGGGTACCACTAACTTGTGAGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
65 AGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* * *
2620791 TTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTATGGGCTTTGAAAA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA
* *
2620856 GAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
66 GAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* *
2620906 TTTGAAAGGAGTGCCACTGAGTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAA
1 TTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
* *
2620970 AGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
65 AGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
2621021 TTTGAAAGGAGTGCCACTGACTTGT-GG----GAAAAG-GTGCCACTGACTTGT-GGCTTTG-AA
1 TTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
* * * *
2621078 AGGGTGTCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGC
65 AGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* *
2621129 TTTAAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
1 TTT-GAAAGGGTGCCACTGACTTGTGGGCTTTGAAA
2621165 GGGATGAACA
Statistics
Matches: 1280, Mismatches: 99, Indels: 57
0.89 0.07 0.04
Matches are distributed among these distances:
108 67 0.05
109 13 0.01
110 16 0.01
111 4 0.00
112 58 0.05
113 50 0.04
114 342 0.27
115 615 0.48
116 34 0.03
117 77 0.06
118 4 0.00
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.29
Consensus pattern (115 bp):
TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA
GAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
Found at i:2622405 original size:1 final size:1
Alignment explanation
Indices: 2622401--2622457 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
2622391 TTTTTTGCTA
* * * * * * *
2622401 TTTTTTCTTTTTTTTTTTGTTTTTTTGTTTTGTTGTTTTTTTTTTGTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2622458 GGGTGTAAAG
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.88
Consensus pattern (1 bp):
T
Found at i:2622408 original size:22 final size:20
Alignment explanation
Indices: 2622383--2622458 Score: 66
Period size: 19 Copynumber: 3.8 Consensus size: 20
2622373 ATCTAGACCC
2622383 TTCTATTTTTTTTTGCTATTTT
1 TTCTATTTTTTTTTG-T-TTTT
*
2622405 TTCTTTTTTTTTTTGTTTTT
1 TTCTATTTTTTTTTGTTTTT
* *
2622425 TTGT-TTTGTTGTTT-TTTTT
1 TTCTATTT-TTTTTTGTTTTT
* *
2622444 TTGTGTTTTTTTTTG
1 TTCTATTTTTTTTTG
2622459 GGTGTAAAGG
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
19 17 0.36
20 15 0.32
21 1 0.02
22 14 0.30
ACGTcount: A:0.03, C:0.04, G:0.11, T:0.83
Consensus pattern (20 bp):
TTCTATTTTTTTTTGTTTTT
Found at i:2622417 original size:13 final size:13
Alignment explanation
Indices: 2622408--2622457 Score: 73
Period size: 13 Copynumber: 3.8 Consensus size: 13
2622398 CTATTTTTTC
2622408 TTTTTTTTTTTGT
1 TTTTTTTTTTTGT
*
2622421 TTTTTTGTTTTGT
1 TTTTTTTTTTTGT
2622434 TGTTTTTTTTTTGT
1 T-TTTTTTTTTTGT
*
2622448 GTTTTTTTTT
1 TTTTTTTTTT
2622458 GGGTGTAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
13 22 0.67
14 11 0.33
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTTGT
Found at i:2622450 original size:16 final size:15
Alignment explanation
Indices: 2622408--2622457 Score: 68
Period size: 14 Copynumber: 3.5 Consensus size: 15
2622398 CTATTTTTTC
2622408 TTTTTTTTTT-TGTT
1 TTTTTTTTTTGTGTT
* *
2622422 TTTTTGTTTTGT-TG
1 TTTTTTTTTTGTGTT
2622436 TTTTTTTTTTGTGTT
1 TTTTTTTTTTGTGTT
2622451 TTTTTTT
1 TTTTTTT
2622458 GGGTGTAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 21 0.70
15 9 0.30
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTTGTGTT
Done.